modify readme to prep for migration to the ADF&G account.

README.md

@@ -1,42 +1,25 @@
 # SusitnaEG
-***
-
-This repository contains the Susitna River spawn-recruit analysis conducted by the Alaska Department of Fish and Game. The repository is organized as follows:
-
-* __SusitnaEG__ A package with data and R code for preparing the analysis and summarizing the results.
-    + The package contains the project data and functions that necessary to prepare the analysis and examine the results. R help files are written for all of the function and their use is demonstrated in 'script_SuChin.r' and 'SusitnaEG_July2018_update.md'. 
-* __markdown__ Markdown files and associated output for various summaries and updates.
-* __models__ Rjags model code. The working file is 'mod_SuChin.r'.
-* __scripts__ R scripts to run the analysis. The working file is 'script_SuChin.r'.
-
-## To reveiw this analysis
-***
-### Static collaboration
-Press the green "clone or download" button followed by the "download ZIP" button. Open the zip file, extract the results and double click the file "SusitnaEG.Rproj". Email me questions, comments or concerns.
-
-### Active collaboration
-This method has some overhead but has advantages that outweigh the costs. You will need do some installation, try reading the first two sections of this guide (http://happygitwithr.com/rstudio-see-git.html). 
-
-1. Fork the development branch of my repository onto your GitHub account.
-![alt text](markdown/READMEpics/Fork.png)
-
-2. In your newly created repository copy the URL (green button labeled 'clone or download' followed by the copy symbol next to the URL).
-
-3. In RStudio navigate to File > New Project > Version Control > Git and:
-    + Paste the URL under 'repository URL' (The directory name will auto-fill)
-    + Pick a location for the directory
-
-4. Run the script, look at the code and results. If you see an, error fix it! If you know a better way, try it!
-
-5. Save the files you have modified. Don't rename anything just save it.
-
-8. Check out the Git pane. Changed files will be listed there. Stage them (staging just means to track them using Git) by checking the box next to each file.
-
-9. Press the commit button (A commit is a snapshot of the project. In this case it is a snapshot after you have made some corrections or modifications). A new window will open summarizing your commit.
-![alt text](markdown/READMEpics/commit.png)
-In this example the files with red boxes were deleted, the files with purple boxes were renamed, the files with green boxes were added and the file with a blue box was modified. The modifications can be seen below (the old code is in pink, the new code is in green). Add a commit message explaining the changes in general terms and press the commit button.
-
-9. You can repeat the modify-stage-commit process as many times as you would like. When you are finished you can push your work back to GitHub (Green Arrow in Rstudio). Pushing applies the changes you have made in the local repository (your computer's hard drive) to your remote repository (stored on GitHub).
-
-10. Go back to GitHub and your SusitnaEG repository. Your changes should be visible. Go to the "Pull Requests" tab and press the green "New Pull Request" button (A Pull request is a way for you to let me know that you have made some improvements and you would like me to consider adding them to the analysis). A summary of your changes will appear. Submit the request and thanks in advance!
-![alt text](markdown/READMEpics/pullrequest.png)
+
+This repository the run reconstruction and stock assessment for Susitna River Chinook salmon.
+
+The network location for this repository is on Anchorage DSF S drive: "S:\RTS\Reimer\SusitnaEG".
+
+The most recent report associated with this analysis can be found at <http://www.adfg.alaska.gov/FedAidPDFs/FMS20-01.pdf>.
+
+The file/folder structure for this analysis is as follows:
+
+-   data/: R data sets created by the R codes located in data-raw/.
+
+-   data-raw/: raw data and data preparation/cleaning functions for the analysis. The main files in this folder are SusitnaEG age.xlsx, SusitnaEG Ha_post95.xlsx, SusitnaEG Hm.xlsx, SusitnaEG regs.xlsx, SusitnaEG sonar.xlsx, SusitnaEG survey.xlsx, and SusitnaEG weirs.xlsx which contain the raw data and need to be updated annually. The other date files in this directory are used in the analysis but represent early time periods and do not require an annual update.
+
+-   docs/: this folder contains the html file which will be hosted on GitHub pages.
+
+-   functions/: table, figure and helper functions for the SR analysis.
+
+-   markdown/: RMarkdown and quarto document associated with this analysis. The 2020 report was prepared using markdown files included in this folder. In addition annual updates to the run reconstruction component (which inform area staff about annual escapements) are including in this folder.
+
+-   models/: Jags code associated with this analysis. The file model_SuChin.R is the main jags code.
+
+-    posts/: Posterior samples from the model. These files are large and not available on GItHUb however the code and data ro replicate each posterior should be available. The posterior sample are stored in the network location indicated above.
+
+-   scripts/: R code to run analysis. The file script_SuChin.R is the main jags code.